BIOC1020 Cellular Biochemistry

Introduction to the common biomolecules:

Monomers and polymers
Andrew Pearson

The biochemistry of functional groups and

bonds
What are functional groups?
The atom or group of atoms that defines the
structure of a particular family of organic
compounds and, at the same time, determines
their properties is called the functional
group. (Morrison & Boyd, Organic Chemistry)

Take a molecule like L-DOPA

It has a number of functional
groups which contribute to its
properties.

Carboxylic acid
?

Carboxylic acid
Amino group
?

Carboxylic acid
Amino group
Methylene group
?

Carboxylic acid
Amino group
Methylene group
Aryl group

Carboxylic acid
Amino group
Methylene group
Aryl group

Hydroxyl group

Properties of functional groups

Carboxylic acids.

Carboxylic acids, like all acids, give up their acidic

protons. They become carboxylate anions.
Such anions can be persuaded to accept protons if the
pH is lower than the pKa value of the group.

Properties of functional groups

Amines.

Amines can accept protons. In fact it is fairly difficult

to get the protons off: a very high pH (= low [H +]) is
needed. If the pH of the surrounding medium is lower
than the pKa of the amine group it will be protonated,
and positively charged.
This is in contrast to the behaviour of acids which are
reluctant to accept protons unless [H+] is high.

Properties of functional groups

Aldehydes.

Aldehyde carbons have a planar rather than the usual

tetrahedral structure. The oxygen nucleus is more
electronegative than the carbon, hence takes more
than its fair share of the double bond electrons. This
thins the electron cloud above and below the carbon
nucleus, exposing it to nucleophilic attack.
Thus aldehydes are said to be quite reactive.

Properties of functional groups

Alcohols.

Alcohols react readily with acids to form esters by the

elimination of water. Hydrolysis of esters requires
little energy.

The same biochemistry is used by all

living cells that have been studied.
Electrons, protons and energy are
the fundamental components of
biochemistry and bioenergetics.

Chemistry fundamentals:
Elements all have different nuclei.
Atomic nuclei are formed of :

protons (+ve charge)

neutrons (no charge)

electrons (-ve charge) are roughly equal
in number to the no. of protons in the
nucleus.
Covalent bonds are the sharing of electrons
between consenting nuclei.

Chemistry
fundamentals:

The s and p orbitals

of electrons closest
to the nuclei of
carbon, hydrogen,
oxygen & nitrogen,
are those most
frequently of
importance in
biochemical bonds,
reactions and
molecules.

The ability of carbon,

oxygen & nitrogen
to form double
bonds gives rise to
- bonding molecular
orbitals.

How strong are chemical bonds

a) relative to each other?
b) relative to other energies?

H-bonds
Electrostatic
Interactions
Van der

Chemistry fundamentals:

Far UV
= 1200 kJ.mol-1
H-bonds
UV = 480 to
343 kJ.mol-1

Electrostatic
Interactions

visible
Near IR =
120 kJ.mol-1

Van der

Far UV = 1200 kJ.mol-1

UV = 480 to
343 kJ.mol-1
Near IR =
120 kJ.mol-1

Amino acids usually means

-amino carboxylic acids

From Brock

From Brock

From Brock

It is the
structure of
the side group
that
distinguishes
amino acids
from each
other.

From Brock

The formation
of a peptide
bond between
two amino acids

From Brock

Enzymes achieve catalysis mainly by:

bringing reactants together in the optimum
orientation, to make new covalent bonds;
or breaking covalent bonds by:
causing the susceptible bond to weaken, by
distorting its angle, or lengthening it;
causing the susceptible bond to weaken by
attacking one of the bonding nuclei
(nucleophilic attack);
causing the susceptible bond to weaken by
withdrawing electrons from it.

 Structures &
functions of
common
carbohydrates

Properties of monosaccharides.
Containing many hydroxyl groups:
sugars interact easily with water:
they are hydrophilic & water-soluble.
Containing many hydroxyl groups:
sugars are highly oxidised and can be
easily hydrolysed into fragments.
Containing many hydroxyl groups:
sugars are easily derivatised to give
related molecules, including aminosugars,
acetylated sugars, dimers, oligomers and
polymers.

From Brock

cis double bonds

between carbons 9
& 10

From Lehninger

Triacylglycerols a.k.a. triglycerides

From Brock